matrix_freq_ratios.c File Reference

Definitions for various scoring matrices' frequency ratios. More...

#include "matrix_freq_ratios.h"
#include "blast_psi_priv.h"

Include dependency graph for matrix_freq_ratios.c:

Go to the source code of this file.

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Macros
#define	BLOSUM62_20A_SCALE_MULTIPLIER   0.9666
	Additional bit scale multiplier for BLOSUM62_20A matrix. More...
#define	BLOSUM62_20B_SCALE_MULTIPLIER   0.9344
	Additional bit scale multiplier for BLOSUM62_20B matrix. More...

Functions
SFreqRatios *	_PSIMatrixFrequencyRatiosNew (const char *matrix_name)
	Retrive the matrix's frequency ratios. More...
SFreqRatios *	_PSIMatrixFrequencyRatiosFree (SFreqRatios *freq_ratios)
	Deallocate the frequency ratios structure. More...

Variables
static const double	BLOSUM45_FREQRATIOS [BLASTAA_SIZE][BLASTAA_SIZE]
	Underlying frequency ratios for BLOSUM45. More...
static const double	BLOSUM50_FREQRATIOS [BLASTAA_SIZE][BLASTAA_SIZE]
	Underlying frequency ratios for BLOSUM50. More...
static const double	BLOSUM62_FREQRATIOS [BLASTAA_SIZE][BLASTAA_SIZE]
	Underlying frequency ratios for BLOSUM62. More...
static const double	BLOSUM80_FREQRATIOS [BLASTAA_SIZE][BLASTAA_SIZE]
	Underlying frequency ratios for BLOSUM80. More...
static const double	BLOSUM90_FREQRATIOS [BLASTAA_SIZE][BLASTAA_SIZE]
	Underlying frequency ratios for BLOSUM90. More...
static const double	PAM30_FREQRATIOS [BLASTAA_SIZE][BLASTAA_SIZE]
	Underlying frequency ratios for PAM30. More...
static const double	PAM70_FREQRATIOS [BLASTAA_SIZE][BLASTAA_SIZE]
	Underlying frequency ratios for PAM70. More...
static const double	PAM250_FREQRATIOS [BLASTAA_SIZE][BLASTAA_SIZE]
	Underlying frequency ratios for PAM250. More...

Detailed Description

Definitions for various scoring matrices' frequency ratios.

Definition in file matrix_freq_ratios.c.

Macro Definition Documentation

BLOSUM62_20A_SCALE_MULTIPLIER

#define BLOSUM62_20A_SCALE_MULTIPLIER   0.9666

Additional bit scale multiplier for BLOSUM62_20A matrix.

Definition at line 1638 of file matrix_freq_ratios.c.

BLOSUM62_20B_SCALE_MULTIPLIER

#define BLOSUM62_20B_SCALE_MULTIPLIER   0.9344

Additional bit scale multiplier for BLOSUM62_20B matrix.

Definition at line 1640 of file matrix_freq_ratios.c.

Function Documentation

_PSIMatrixFrequencyRatiosFree()

SFreqRatios* _PSIMatrixFrequencyRatiosFree

(

SFreqRatios *

freq_ratios

)

Deallocate the frequency ratios structure.

Definition at line 1742 of file matrix_freq_ratios.c.

References _PSIDeallocateMatrix(), BLASTAA_SIZE, SFreqRatios::data, NULL, and sfree.

Referenced by _PSIComputeFreqRatios(), _PSIComputeFreqRatiosFromCDs(), _PSIConvertFreqRatiosToPSSM(), _PSIMatrixFrequencyRatiosNew(), BOOST_AUTO_TEST_CASE(), Kappa_posSearchItemsFree(), s_BuildCompressedScoreMatrix(), s_GetPosBasedStartFreqRatios(), and s_GetStartFreqRatios().

_PSIMatrixFrequencyRatiosNew()

SFreqRatios* _PSIMatrixFrequencyRatiosNew

(

const char *

matrix_name

)

Retrive the matrix's frequency ratios.

Parameters

matrix_name

Available options include: BLOSUM62 BLOSUM62_20 BLOSUM62_20A BLOSUM62_20B BLOSUM45 BLOSUM80 BLOSUM50 BLOSUM90 PAM30 PAM70 PAM250

Returns

NULL on error

Definition at line 1643 of file matrix_freq_ratios.c.

References _PSIAllocateMatrix(), _PSIMatrixFrequencyRatiosFree(), ASSERT, SFreqRatios::bit_scale_factor, BLASTAA_SIZE, BLOSUM45_FREQRATIOS, BLOSUM50_FREQRATIOS, BLOSUM62_20A_SCALE_MULTIPLIER, BLOSUM62_20B_SCALE_MULTIPLIER, BLOSUM62_FREQRATIOS, BLOSUM80_FREQRATIOS, BLOSUM90_FREQRATIOS, SFreqRatios::data, i, malloc(), NULL, PAM250_FREQRATIOS, PAM30_FREQRATIOS, PAM70_FREQRATIOS, and strcasecmp.

Referenced by _PSIComputeFreqRatios(), _PSIComputeFreqRatiosFromCDs(), _PSIConvertFreqRatiosToPSSM(), BOOST_AUTO_TEST_CASE(), Kappa_posSearchItemsNew(), s_BuildCompressedScoreMatrix(), s_GetPosBasedStartFreqRatios(), and s_GetStartFreqRatios().

Variable Documentation

BLOSUM45_FREQRATIOS

const double BLOSUM45_FREQRATIOS[BLASTAA_SIZE][BLASTAA_SIZE]

static

Underlying frequency ratios for BLOSUM45.

Definition at line 38 of file matrix_freq_ratios.c.

Referenced by _PSIMatrixFrequencyRatiosNew().

BLOSUM50_FREQRATIOS

const double BLOSUM50_FREQRATIOS[BLASTAA_SIZE][BLASTAA_SIZE]

static

Underlying frequency ratios for BLOSUM50.

Definition at line 238 of file matrix_freq_ratios.c.

Referenced by _PSIMatrixFrequencyRatiosNew().

BLOSUM62_FREQRATIOS

const double BLOSUM62_FREQRATIOS[BLASTAA_SIZE][BLASTAA_SIZE]

static

Underlying frequency ratios for BLOSUM62.

Definition at line 438 of file matrix_freq_ratios.c.

Referenced by _PSIMatrixFrequencyRatiosNew().

BLOSUM80_FREQRATIOS

const double BLOSUM80_FREQRATIOS[BLASTAA_SIZE][BLASTAA_SIZE]

static

Underlying frequency ratios for BLOSUM80.

Definition at line 638 of file matrix_freq_ratios.c.

Referenced by _PSIMatrixFrequencyRatiosNew().

BLOSUM90_FREQRATIOS

const double BLOSUM90_FREQRATIOS[BLASTAA_SIZE][BLASTAA_SIZE]

static

Underlying frequency ratios for BLOSUM90.

Definition at line 838 of file matrix_freq_ratios.c.

Referenced by _PSIMatrixFrequencyRatiosNew().

PAM250_FREQRATIOS

const double PAM250_FREQRATIOS[BLASTAA_SIZE][BLASTAA_SIZE]

static

Underlying frequency ratios for PAM250.

Definition at line 1438 of file matrix_freq_ratios.c.

Referenced by _PSIMatrixFrequencyRatiosNew().

PAM30_FREQRATIOS

const double PAM30_FREQRATIOS[BLASTAA_SIZE][BLASTAA_SIZE]

static

Underlying frequency ratios for PAM30.

Definition at line 1038 of file matrix_freq_ratios.c.

Referenced by _PSIMatrixFrequencyRatiosNew().

PAM70_FREQRATIOS

const double PAM70_FREQRATIOS[BLASTAA_SIZE][BLASTAA_SIZE]

static

Underlying frequency ratios for PAM70.

Definition at line 1238 of file matrix_freq_ratios.c.

Referenced by _PSIMatrixFrequencyRatiosNew().